Preferably run it on the gel along with the other samples. If this is not
possible, then simply designate any other sample as the wild type and compare
against that.

It is also possible to get Gap4 to produce a consensus trace. This requires
using Pregap4 twice. Firstly process the sequences through Pregap4 will all
the appropriate options except with the mutation detection module disabled.
Assemble these sequences into Gap4. Within Gap4, for each contig start up the
Contig Editor and select Save Consensus Trace from the command menu. This will
produce a trace which is the average of the traces in that contig. Then
delete the Gap4 database and reprocess the sequences using Pregap4, this time
using mutation detection to compare against the consensus trace.